A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations

Abstract The study of very large biomolecular systems over extended spatial and temporal scales is being accomplished through the use of coarse-grained (CG) models. The successes of several CG models, including MARTINI and CMM-CG, and their implementation in current molecular dynamics (MD) software are discussed. In addition, we highlight multiscale CG and mixed all-atom‐CG models for MD simulations. The overall appeal of CG methods is the accessibility of broader temporal and spatial scales for biomolecular and polymer systems. However, care must be taken to fully understand the advantages, assumptions, and limitations of each method. Not all CG models are created equally, and care must be taken when preparing the system and choosing the method of coarse-graining. It is the aim of this review to provide a background and guide to readers as they think about coarse-graining. An outlook to the future of CG simulations is presented in the summary as well as a specific example of how we plan on using CG techniques to explore extended dynamics of membrane-bound transporter proteins.

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